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- PDB-6wmk: Crystal structure of beta sheet heterodimer LHD29 -

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Basic information

Entry
Database: PDB / ID: 6wmk
TitleCrystal structure of beta sheet heterodimer LHD29
Components
  • Beta sheet heterodimer LHD29 - Chain A
  • Beta sheet heterodimer LHD29 - Chain B
KeywordsDE NOVO PROTEIN / Transferrin / DE NOVO DESIGN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBera, A.K. / Sahtoe, D.D. / Kang, A. / Sankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Reconfigurable asymmetric protein assemblies through implicit negative design.
Authors: Sahtoe, D.D. / Praetorius, F. / Courbet, A. / Hsia, Y. / Wicky, B.I.M. / Edman, N.I. / Miller, L.M. / Timmermans, B.J.R. / Decarreau, J. / Morris, H.M. / Kang, A. / Bera, A.K. / Baker, D.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sheet heterodimer LHD29 - Chain A
B: Beta sheet heterodimer LHD29 - Chain B
C: Beta sheet heterodimer LHD29 - Chain A
D: Beta sheet heterodimer LHD29 - Chain B


Theoretical massNumber of molelcules
Total (without water)32,6134
Polymers32,6134
Non-polymers00
Water88349
1
A: Beta sheet heterodimer LHD29 - Chain A
B: Beta sheet heterodimer LHD29 - Chain B


Theoretical massNumber of molelcules
Total (without water)16,3062
Polymers16,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8 kcal/mol
Surface area7440 Å2
MethodPISA
2
C: Beta sheet heterodimer LHD29 - Chain A
D: Beta sheet heterodimer LHD29 - Chain B


Theoretical massNumber of molelcules
Total (without water)16,3062
Polymers16,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-7 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.072, 38.175, 60.379
Angle α, β, γ (deg.)90.000, 98.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta sheet heterodimer LHD29 - Chain A


Mass: 8286.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Beta sheet heterodimer LHD29 - Chain B


Mass: 8019.950 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→44.22 Å / Num. obs: 12352 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 0.971 / Net I/σ(I): 5.2
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1996 / CC1/2: 0.468 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed Model

Resolution: 2.2→38.03 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.0305
RfactorNum. reflection% reflection
Rfree0.2832 597 4.84 %
Rwork0.2536 --
obs0.2551 12330 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 49 2154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022137
X-RAY DIFFRACTIONf_angle_d0.39382876
X-RAY DIFFRACTIONf_chiral_restr0.0377321
X-RAY DIFFRACTIONf_plane_restr0.0014366
X-RAY DIFFRACTIONf_dihedral_angle_d23.663794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.37191420.29953059X-RAY DIFFRACTION98.34
2.42-2.770.35021570.32162981X-RAY DIFFRACTION96.7
2.77-3.490.31421500.27982906X-RAY DIFFRACTION93.2
3.49-38.030.24011480.21972787X-RAY DIFFRACTION87.51

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